def parse_bc won't read barcodes

thomasvangurp / epiGBS

Code for working with epiGBS data

MIT License

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def parse_bc won't read barcodes #1

Closed AlvarezMF closed 8 years ago

AlvarezMF commented 8 years ago

Prints a length of zero at the end - it looks like it's not properly reading the barcodes into the bc_dict dictionary, resulting in an empty dictionary. I'm attaching our barcodes file in .csv format, but we've tried tab-delimited as well. This results in empty files created at the end of the script.

barcodes.csv.zip

AlvarezMF commented 8 years ago

Scratch that, solved by updating line 217 to: file_in = open(barcodes, 'rU')

also, had to feed it a tab-delineated file, although it defaults to a .csv file.

thomasvangurp commented 8 years ago

I'm reworking many of the scripts to make sure dependency and other issues are tackled.